3R5T

Crystal structure of holo-ViuP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unique iron coordination in iron-chelating molecule vibriobactin helps Vibrio cholerae evade mammalian siderocalin-mediated immune response.

Li, N.Zhang, C.Li, B.Liu, X.Huang, Y.Xu, S.Gu, L.

(2012) J Biol Chem 287: 8912-8919

  • DOI: 10.1074/jbc.M111.316034
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Iron is essential for the survival of almost all bacteria. Vibrio cholerae acquires iron through the secretion of a catecholate siderophore called vibriobactin. At present, how vibriobactin chelates ferric ion remains controversial. In addition, the ...

    Iron is essential for the survival of almost all bacteria. Vibrio cholerae acquires iron through the secretion of a catecholate siderophore called vibriobactin. At present, how vibriobactin chelates ferric ion remains controversial. In addition, the mechanisms underlying the recognition of ferric vibriobactin by the siderophore transport system and its delivery into the cytoplasm specifically have not been clarified. In this study, we report the high-resolution structures of the ferric vibriobactin periplasmic binding protein ViuP and its complex with ferric vibriobactin. The holo-ViuP structure reveals that ferric vibriobactin does not adopt the same iron coordination as that of other catecholate siderophores such as enterobactin. The three catechol moieties donate five, rather than six, oxygen atoms as iron ligands. The sixth iron ligand is provided by a nitrogen atom from the second oxazoline ring. This kind of iron coordination results in the protrusion of the second catechol moiety and renders the electrostatic surface potential of ferric vibriobactin less negatively polarized compared with ferric enterobactin. To accommodate ferric vibriobactin, ViuP has a deeper subpocket to hold the protrusion of the second catechol group. This structural characteristic has not been observed in other catecholate siderophore-binding proteins. Biochemical data show that siderocalin, which is part of the mammalian innate immune system, cannot efficiently sequester ferric vibriobactin in vitro, although it can capture many catecholate siderophores with high efficiency. Our findings suggest that the unique iron coordination found in ferric vibriobactin may be utilized by some pathogenic bacteria to evade the siderocalin-mediated innate immune response of mammals.


    Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferric vibriobactin ABC transporter, periplasmic ferric vibriobactin-binding protein
A
305Vibrio choleraeMutation(s): 0 
Gene Names: viuPVC_0776C9J66_11805ERS013140_02227ERS013165_02595ERS013186_02145ERS013199_00569ERS013202_00573ERS013206_00558
Find proteins for Q9RCF6 (Vibrio cholerae)
Go to UniProtKB:  Q9RCF6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VBN
Query on VBN

Download CCD File 
A
(4S,5R)-N-{3-[(2,3-dihydroxybenzoyl)amino]propyl}-2-(2,3-dihydroxyphenyl)-N-[3-({[(4S,5R)-2-(2,3-dihydroxyphenyl)-5-methyl-4,5-dihydro-1,3-oxazol-4-yl]carbonyl}amino)propyl]-5-methyl-4,5-dihydro-1,3-oxazole-4-carboxamide
C35 H39 N5 O11
LLMKLMMXMOTPRU-QCOILQKOSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MOH
Query on MOH

Download CCD File 
A
METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VBNKd:  2.6500000953674316   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.496α = 90
b = 55.545β = 117.02
c = 69.542γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references